LOCUS       NZ_CP066441             4305 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 66 plasmid p66_4kb, complete
            sequence.
ACCESSION   NZ_CP066441
VERSION     NZ_CP066441.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038081
            Assembly: GCF_016406405.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4305)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4305)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2020) Biological Sciences, University of Texas at
            Dallas, 1520 Richardson Dr Apt 1418, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 131.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 03:34:42
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,204
            CDSs (total)                      :: 3,112
            Genes (coding)                    :: 2,993
            CDSs (with protein)               :: 2,993
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 119
            CDSs (without protein)            :: 119
            Pseudo Genes (ambiguous residues) :: 0 of 119
            Pseudo Genes (frameshifted)       :: 43 of 119
            Pseudo Genes (incomplete)         :: 67 of 119
            Pseudo Genes (internal stop)      :: 32 of 119
            Pseudo Genes (multiple problems)  :: 19 of 119
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066441.1.
            Bacteria and source DNA available from Dr. Kelli Palmer, UTDallas.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4305
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 66"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p66_4kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            complement(join(3357..4305,1..458))
                     /locus_tag="JCP89_RS15870"
                     /old_locus_tag="JCP89_15860"
     CDS             complement(join(3357..4305,1..458))
                     /locus_tag="JCP89_RS15870"
                     /old_locus_tag="JCP89_15860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_002304901.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQINIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKMEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSDELRYICRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(680..1042)
                     /locus_tag="JCP89_RS15875"
                     /old_locus_tag="JCP89_15865"
     CDS             complement(680..1042)
                     /locus_tag="JCP89_RS15875"
                     /old_locus_tag="JCP89_15865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002313294.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVGNELRADEKSAPSERNYPNESDGIFGGIPNRKSQ
                     MSESGFASMFSDVNSR"
                     /name="hypothetical protein"
     gene            complement(1046..1354)
                     /locus_tag="JCP89_RS15880"
                     /old_locus_tag="JCP89_15870"
     CDS             complement(1046..1354)
                     /locus_tag="JCP89_RS15880"
                     /old_locus_tag="JCP89_15870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292673.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002304909.1"
                     /translation="MDKIDLREETVNRIEVMYERLADYLNLSDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISVINSKEKGM"
                     /name="hypothetical protein"
     gene            complement(1363..1782)
                     /locus_tag="JCP89_RS15885"
                     /old_locus_tag="JCP89_15875"
     CDS             complement(1363..1782)
                     /locus_tag="JCP89_RS15885"
                     /old_locus_tag="JCP89_15875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            complement(1779..2768)
                     /locus_tag="JCP89_RS15890"
                     /old_locus_tag="JCP89_15880"
     CDS             complement(1779..2768)
                     /locus_tag="JCP89_RS15890"
                     /old_locus_tag="JCP89_15880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002304903.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="protein rep"
     Typing          complement(4..551)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.071"
                     /coverage="99.0"
                     /evalue="8.95e-102"
     Typing          complement(3361..4304)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.365"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtagacgg ataaactagg attccgttct ttaaattctt tgaaatactc aactaaaatt
       61 ttgttggcaa tcactcgatt ttgttctgct tgttgttccg atatgccagt agaagaacca
      121 tcatcacgag tagtacgaaa atcatcaaga gtaccaattt gcacgataaa ttctcgctgt
      181 ggttccattt ttttatcctt gcgaaccttt gctaaatagt cctcaatttt tctatcggct
      241 cttttctgct ttgcattata tttttctacg gcttcaccga ataattcttc atatttttca
      301 cgaatattta tttgttccaa atagatattt tcatccgatt ttgtgaaatc aatatgctta
      361 tgccagtcat tgattttttg gctatcagtt aactcacgat tattatgaga aatgcttgta
      421 ttctttgttc cctttttgaa cgaaatacta aaccccaagt taaacccctc cttcgcgctg
      481 tcgctaataa aaagagtgta aacctttctg ttactctttg tcaaagagta acgttttcct
      541 aattgtgaca tgactgtcac aattccaaac gctctccgag ggttttcgcc gtcacaagtg
      601 acaacgaaaa aaggagccga aagcgtgtca cgctctcaac tccttttacg ctttattttg
      661 cttcatgcaa aatattcgct tatcgtgaat ttacgtcact aaacattgac gcaaatccac
      721 tctcactcat ctgacttttt ctattcggta tccctccgaa tattccgtca gattcgttag
      781 ggtaattccg ttcgcttggt gctgattttt catcagctcg caactcatta cccactgatt
      841 tttcgtgttg ctgatcgtca gaaatcgacg atagccaccg ctcaaaatca gcaaaagatt
      901 caaacccaaa acgcttgcga agagccttgc ccattgcagc attttctttc tcaatcaatc
      961 gtttcttctg ttggcgaagt ttcgcctgtt ctttttttaa tttttcttct tgcactttaa
     1021 tatctgctaa agtcattccc ataaactaca tccccttttc tttggaatta ataacggaaa
     1081 tttggtttaa ctgcataata tgactcatta atttcaacca aaattctttt tcagcttcat
     1141 cagttgtttg cgctaaatgc ttatgaacaa attcattagt caaaactgaa gattttgcta
     1201 gatcagcatt gataaccgag ttgagaacat ccatcattcg ttcaagcatc tcactataat
     1261 tatcttcatc cgaaagattc aaataatcag ctaaccgttc atacatcact tcaattctat
     1321 tgactgtttc ttctctcaaa tcaattttat ccatgtcaca tctcacttcc agaattgcca
     1381 ccattttcga ttttttaatt cttgattttc tagtaacaac tgatcgtttt tttgttgctg
     1441 aagcagggtc aatttttgtt gatcacgaat catttctgtt aattcagaaa tatgtttgtc
     1501 cttctcagct aattgatcac gcaaaaactc attctctttt tccaaaggaa aatcactgcc
     1561 cgtgctattg accggtaaat gaccagtcaa ttgaccacct tttgaccgat aaattgaccg
     1621 agcaacacca atcaactctt tgtctagcaa gataattcca tttttcttgt accgagcaag
     1681 atcatatccg gctttgacta gataatttct cactgtattt ttggttattc ctagttcatc
     1741 agcaagcgcc ttaattgtca ttttatccgt tgaatcagtc attcattttc cccctcaaca
     1801 gatttttcat cgacatacat tcctgaaaaa taatttcttt catcagcact catctcacga
     1861 taatcaaccg catatttcga ttctttcctc atccacgaag cagtcaaaaa ccaaaaatat
     1921 tcattctcat cttttttctt ataacgatca aggtcacccg actcatattt tttcttgtat
     1981 tctttgaata caccgttaaa cgtaatcaac tgacgacctt tcattgcatg atagaatgtg
     2041 tcaaacactt cctgactttc ggtcagttca aaatcttttg ccgaatattt cgcaacttcc
     2101 tgtactgctt tttcttgttg gaaccctttg accttgcgaa tatccaactg ggtaatttcg
     2161 tcggtaccat ccggattaat tcccgttttt ccggtcactt cccgccacaa atctaaccat
     2221 tccgattgct tgatataata atctttatcc gtgaaataag atttatttac tgccaaaatc
     2281 aagtgaaaat gcgggttata gtcattccgt tttttgttgt acgtgatttc caattttcgc
     2341 acatagcctt taatcgaagt cttaacccgt ttgcgcataa acatcttttt caatgcatga
     2401 ttaaacaaat caatttcatc gttcaaacat tccgctttta cattcggtgt cgtcaacgtc
     2461 ataaaaataa attgatactg cttttcttcc gcaatagctt gcatcataat cgacaacatc
     2521 atcgaatcct tacgagcttt acgccaagca cataacggac agaaacgatt tttacaaaag
     2581 tgagcttgga ccaatttctt tttctcctta tcaatcgttg caataaattc taaatatgaa
     2641 ccacagcctg tcatcaattc acgcattttg ggagaaattc gattatcact aaatgccacc
     2701 acttttttca aatttttctt tttttctcga aatgttccgt taatcaaatc ttgctttttc
     2761 tttttcatct tgctatactg aatctacaaa ttttgtatac aaaaaaggct gaaaagccga
     2821 taacaaaaaa tagattgctc tcctttctag tttagttttt ttctagtcaa ttaaaactat
     2881 aaaatactag ggaagaaaaa gcaatctttt tttttgttct tccttagagc cacaagggat
     2941 agacccatac tatagccccg atttcttcgc agaaatagtt gcctatagta tcaagataag
     3001 aaaaaacatc aaaaaagagg gcgaaaatcg cccccttttt ttcgttttaa aaccccaaaa
     3061 cccaaagaca taaaattcga tcaatcgacc actgcatttt taagggggtg tacatatttt
     3121 gtacatttaa ccgcctgtta gatagggctg ttaaattttc ccactcattc ttagtcatgc
     3181 aaacataaaa ccgcaccctt taaaaagggc gcccccaaac ttcgctaacg ctaagttggc
     3241 caaaaaatgg acttgccatt ttttagcaaa tgtcagctta ataggctagt ggtttagccg
     3301 tcaactcctt atcctcggca caaaccgcct ccggtaccgt tgactgcaca tcgtaactac
     3361 cactcgatct catcttcaga acgctctaat ttatgctgtg agacgttttg acgataaaat
     3421 aaggttttct cctgctctaa tacttctaat tcctcagaaa gccccatatc cttttctgca
     3481 agcccaaaac ggatagacaa acgagtgatc gatttttgaa atgcgttttt taatcgctct
     3541 aaacgctggc gtaaagagcg attttcttct ttcagctttt tattttccac ttgtaaatct
     3601 gctaattgtt ttctaccaga caaatgacgc tcttcttcca atgcagctac atactcattt
     3661 aattctgtat tttgctcaag catctgtaaa tattgctcac tcatgttatc agcatttctc
     3721 ttggcatttg ttgctctcgt agctcgttga tacaaatcaa caaaatcatt cccagataaa
     3781 tgatacgaac catcaggaag cctcttgaaa ctttctaaag gaaccatatc tttttggaaa
     3841 atgaccgcca tctctttttt tacattcagc atatttttct tctcttcttc aatcttcgct
     3901 ctctcagaag ccaccagagc cttctcacgc tcgttttctt ctctttgcct acaaatatac
     3961 ctcaactcat cagaaacgct ctcacgctct tttacggccg tttgacgcaa ttcggaaatt
     4021 tcgctcatga tttctttgta ttcatgaata tctttgattt tgttagtacc gactaactca
     4081 cgctcccaac caaaatctgc catcaaacgt tcaattgact caacttcctg attcctaaaa
     4141 ttattccaaa tcactcgacc attctcttta tctgctcgta aaccctgctg ttgcaaggct
     4201 ttgttaaaac ttggttgctt ttgaacaccc cgtttatacc cttcagcaac aggaacaata
     4261 ttcaaatgca ggtgcggact tacttcgtca ttatgaataa cagca
//
